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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCAGCTGAGAGTCTGGATAGTTTTACTCTCATTTATACAAATATTCTGGAACATCAACCAGATTGCCCGgtaattttttcaacaagctactcgattttgccagaaattagtggtttagtagtgcattcatttctgttgatgtgctgaacttgatatctacgttatgtag

Basic information

species Oryza sativa
transcript LOC_Os02g51430.1
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g51430.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G070045_T01 (Zea mays), 5'ss of exon 18
GCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCAGCTGAGAGTCTGGATAGTTTTACTCTCATTTATACAAATATTCTGGAACATCAACCAGATTGCCCGgtaatttttt---caacaagc-tactcgattttgccagaaattagtggttt----------agtagtgcattcatttctgttgatgtgctg-aacttgatatctacgttatgtag
|||||||||||| ||| | |||||||| ||||||||||||||| ||||||| |||||||||||||| || ||||| |||||||||||||| ||||||||||||||||| |    |||||   || | |  || || |    ||  | ||||          |  ||  | ||  ||||   | |||  ||  ||||||| |||| |||| | |||
GCGGATTCTGGCAGATATGAGGGAGCTAGCTTCAGCTGAGAGTTTGGATAGCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttctgcctaacaaatatatttggcttcgctaatgcttgattgttttaaaatatgaaacagctcgttattttcccgttatgccctacaacttgacatctgcgttttttag

upper sequence: LOC_Os02g51430.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G161553_T01 (Zea mays), 5'ss of exon 5
GCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCAGCTGAGAGTCTGGATAGTTTTACTCTCATTTATACAAATATTCTGGAACATCAACCAGATTGCCCGgtaatttttt---caacaagc-tactcgattttgccagaaattagtggtttagtagtgc--attcatttctgttgatgtgctgaacttgatatctacgttatgtag-----------------------------------------------------------------------------------------
|||||||||||| ||| | || || || |||||||||| |||| ||||||| |||||||||||||  |||||||| |||||||||||||| ||||||||||||||||| |    |||||   || ||   ||||| |    ||     || |  | |    |   || |  |    | |||     || ||  ||  |  |                                                                                              
GCGGATTCTGGCAGATATGAGAGATCTAGCTTCAGCTGGGAGTTTGGATAGCTTTACTCTCATTTTCACAAATATACTGGAACATCAACCTGATTGCCCGgtaattttctgcctaacaaatatattcagctttgctaatgctttactattgaaaaatatgaaacaatatgagcctctctgcatcggtttatccctttgccagactccactcctgggagagactctggcattggatttgtccttttttatgttaatttctcgttatgtcctacaacttgacatctgtgttttttag

upper sequence: LOC_Os02g51430.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GLYMA03G03120.2 (Glycine max), 5'ss of exon 24
GCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCAGCTGAGAGTCTGGATAGTTTTACTCTCATTTATACAAATATTCTGGAACATCAACCAGATTGCCCGgtaattttttcaacaagcta--ctcgattttgccagaaattagtg-gtttagtagtgcattcatttctgttgatgtgctgaact-tgatatctacgttatgtag
| |  | ||    ||  | ||||||||||||||||| ||||| |||||||  ||||| ||||| ||||||||||| || ||||||||||| || ||||||||||  || |   ||| |||  ||| |||||  ||   |  | ||  | ||  ||| | || |    |    || |  |   |  ||   |  | |||||    
GAGTGTACTTAGCGACTTGAGGGAGCTTGCTTCAGCAGAGAGCCTGGATACCTTTACACTCATCTATACAAATATACTCGAACATCAACCTGACTGCCCGgtaaaattatgcccaatctaatctcaatttttgcattcacaaatgcatgtatgagttctttaagcagttgaaatattttttgcagtgggtttcaagttat----

upper sequence: LOC_Os02g51430.1 (Oryza sativa), 5'ss of exon 23
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 5'ss of exon 23
GCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCAGCTGAGAGTCTGGATAGTTTTACTCTCATTTATACAAATATTCTGGAACATCAACCAGATTGCCCGgtaattttttcaacaagctactcgattttgccagaaattagtggtttagtagtgcattcatttctgttgatgtgctga--acttgatatctac--gttatgtag
  |||| |||  |||  | || ||||||||||| || ||||| ||||||| ||| || ||||| || ||||| ||||| ||||||||||| ||||| || |||| |  |   | ||       | |  ||  ||  |  | |  ||| ||  ||   |  |   | |  |  | |  |  || | ||| |  |  | ||| |  
CAGGATACTGAGTGACTTGAGAGAGCTTGCTTCCGCAGAGAGCCTGGATACTTTCACACTCATCTACACAAACATTCTTGAACATCAACCCGATTGTCCAgtaagtgctattaaaaatagt--gttcatggtagtgaccatt--tttcgttttgtggttctgagtatcaaattccaaataacctaatagcctctagctattttc

upper sequence: LOC_Os02g51430.1 (Oryza sativa), 5'ss of exon 23
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 5'ss of exon 23
GCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCAGCTGAGAGTCTGGATAGTTTTACTCTCATTTATACAAATATTCTGGAACATCAACCAGATTGCCCGgtaattttttcaacaagctactcgattttgccagaaattagtggtttagtagtgcattcatttc-tgttgatgtgctgaacttgatatctacgttatgtag--
  |||| |||  |||  | || ||||||||||| || ||||| |||||||  || || ||||| || ||||| ||||| ||||||||||| ||||| || |||| |  |   | ||       | |  ||  ||  |   ||    | ||||||      |||| | |||  || ||||   | | |       ||   |   
CAGGATACTGAGTGACTTGAGAGAGCTTGCTTCTGCAGAGAGCCTGGATACATTCACACTCATATACACAAACATTCTTGAACATCAACCTGATTGTCCAgtaagtgctattaaaaatagt--gttcatggtagtgacc-gtttcatggtagtgaccgtttttcattttgtagttctgagtatcaaactctaaataaccatca

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|87031003|gb|CI270151.1|CI270151
EST:     GTTTTACTCTCATTTATACAAATATTCTGGAACATCAACCAGATTGCCCG                         CCTGAGGTTGTTGAGAAGCTTGTGGGAATGAGGGAAGGCATTCCAAGGAAG
genomic: GTTTTACTCTCATTTATACAAATATTCTGGAACATCAACCAGATTGCCCGgtaatttttt ... cgttatgtagCCTGAGGTTGTTGAGAAGCTTGTGGGAATGAGGGAAGGCATTCCAAGGAAG
EST: gi|86482093|gb|CI124726.1|CI124726
EST:     GTTTTACTCTCATTTATACCAATATTCTGGAACATCAACCAGATTGCCCG                         CCTGAGGTTGTTGAGAAGCTTGTGGGAATGAGGGAAGGCATTCCAAGGAAG
genomic: GTTTTACTCTCATTTATACAAATATTCTGGAACATCAACCAGATTGCCCGgtaatttttt ... cgttatgtagCCTGAGGTTGTTGAGAAGCTTGTGGGAATGAGGGAAGGCATTCCAAGGAAG
EST: gi|86855814|gb|CI271033.1|CI271033
EST:     GTTTTACTCTCATTTATACAAATATTCTGGAACATCAACCAGATTGCCCG                         CCTGAGGTTGTTGAGAAGCTTGTGGGAATGAGGGAAGGCATTCCAAGGAAG
genomic: GTTTTACTCTCATTTATACAAATATTCTGGAACATCAACCAGATTGCCCGgtaatttttt ... cgttatgtagCCTGAGGTTGTTGAGAAGCTTGTGGGAATGAGGGAAGGCATTCCAAGGAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 61 (upstream exon), 28 (downstream exon)
Score: 3

GCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCAGCTGAGAGTCTGGATAGTTTTACTCTCATTTATACAAATATTCTGGAACATCAACCAGATTGCCCGgtaatttttt ... cgttatgtagCCTGAGGTTGTTGAGAAGCTTGTGGGAATGAGGGAAGGCATTCCAAGGAAGGAAGCCAAAGAG




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